Opened 7 months ago
Closed 7 months ago
#17209 closed defect (can't reproduce)
RMSD header index error when restoring session
Reported by: | Owned by: | pett | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Sessions | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.19044 ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > D:\TaxolManuscript\TaxolMTMap\StructuralFigure1\DimerRise\b3GDPvsTaxol.cxs > format session Unable to restore session, resetting. Traceback (most recent call last): File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 757, in restore obj = sm.restore_snapshot(self, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\tool.py", line 827, in restore_snapshot inst._finalize_init(data['alignment']) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\tool.py", line 167, in _finalize_init self.seq_canvas = SeqCanvas(parent, self, self.alignment) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 205, in __init__ self.layout_alignment() File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 783, in layout_alignment self.lead_block = SeqBlock(label_scene, self.main_scene, None, self.font, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__ self.next_block = SeqBlock(label_scene, main_scene, self, self.font, self.emphasis_font, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__ self.next_block = SeqBlock(label_scene, main_scene, self, self.font, self.emphasis_font, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__ self.next_block = SeqBlock(label_scene, main_scene, self, self.font, self.emphasis_font, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [Previous line repeated 83 more times] File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 1645, in __init__ self.layout_lines(headers, self.header_label_color) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 2342, in layout_lines self._layout_line(line, label_color, bli, end) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 2319, in _layout_line item = self.make_item(line, self.seq_offset + i, xs[i], ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 2400, in make_item info = line.depiction_val(offset) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\alignment_headers\rmsd.py", line 70, in depiction_val val = self[pos] ~~~~^^^^^ IndexError: list index out of range Traceback (most recent call last): File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 757, in restore obj = sm.restore_snapshot(self, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\tool.py", line 827, in restore_snapshot inst._finalize_init(data['alignment']) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\tool.py", line 167, in _finalize_init self.seq_canvas = SeqCanvas(parent, self, self.alignment) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 205, in __init__ self.layout_alignment() File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 783, in layout_alignment self.lead_block = SeqBlock(label_scene, self.main_scene, None, self.font, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__ self.next_block = SeqBlock(label_scene, main_scene, self, self.font, self.emphasis_font, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__ self.next_block = SeqBlock(label_scene, main_scene, self, self.font, self.emphasis_font, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__ self.next_block = SeqBlock(label_scene, main_scene, self, self.font, self.emphasis_font, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [Previous line repeated 83 more times] File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 1645, in __init__ self.layout_lines(headers, self.header_label_color) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 2342, in layout_lines self._layout_line(line, label_color, bli, end) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 2319, in _layout_line item = self.make_item(line, self.seq_offset + i, xs[i], ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 2400, in make_item info = line.depiction_val(offset) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\alignment_headers\rmsd.py", line 70, in depiction_val val = self[pos] ~~~~^^^^^ IndexError: list index out of range During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest self._callback(info) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept return interceptor(request_info, *args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 353, in intercept chimerax_intercept(*args, view=view, session=session) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 455, in chimerax_intercept session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\gui.py", line 423, in thread_safe func(*args, **kw) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 446, in defer cxcmd(session, topic) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd run(session, cmd) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\commands\run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 131, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 213, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 514, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 484, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core_formats\\__init__.py", line 37, in open return cxs_open(session, data, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 1027, in open session.restore(stream, path=path, resize_window=resize_window, combine=combine) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 765, in restore self.reset() File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 552, in reset sm.reset_state(container, self) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seqalign\manager.py", line 273, in reset_state alignment._destroy() File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seqalign\alignment.py", line 724, in _destroy self._notify_observers(self.NOTE_DESTROYED, None) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seqalign\alignment.py", line 823, in _notify_observers recipient.alignment_notification(note_name, note_data) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\tool.py", line 471, in alignment_notification self.delete() File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\tool.py", line 509, in delete self.region_manager.destroy() ^^^^^^^^^^^^^^^^^^^ AttributeError: 'SequenceViewer' object has no attribute 'region_manager' AttributeError: 'SequenceViewer' object has no attribute 'region_manager' File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\tool.py", line 509, in delete self.region_manager.destroy() ^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. > open > D:\TaxolManuscript\TaxolMTMap\StructuralFigure1\DimerRise\b3GDPvsTaxol.cxs > format session Unable to restore session, resetting. Traceback (most recent call last): File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 723, in restore self.reset() File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 552, in reset sm.reset_state(container, self) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seqalign\manager.py", line 273, in reset_state alignment._destroy() File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seqalign\alignment.py", line 724, in _destroy self._notify_observers(self.NOTE_DESTROYED, None) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seqalign\alignment.py", line 823, in _notify_observers recipient.alignment_notification(note_name, note_data) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\tool.py", line 471, in alignment_notification self.delete() File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\tool.py", line 509, in delete self.region_manager.destroy() ^^^^^^^^^^^^^^^^^^^ AttributeError: 'SequenceViewer' object has no attribute 'region_manager' Traceback (most recent call last): File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 723, in restore self.reset() File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 552, in reset sm.reset_state(container, self) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seqalign\manager.py", line 273, in reset_state alignment._destroy() File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seqalign\alignment.py", line 724, in _destroy self._notify_observers(self.NOTE_DESTROYED, None) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seqalign\alignment.py", line 823, in _notify_observers recipient.alignment_notification(note_name, note_data) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\tool.py", line 471, in alignment_notification self.delete() File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\tool.py", line 509, in delete self.region_manager.destroy() ^^^^^^^^^^^^^^^^^^^ AttributeError: 'SequenceViewer' object has no attribute 'region_manager' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest self._callback(info) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept return interceptor(request_info, *args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 353, in intercept chimerax_intercept(*args, view=view, session=session) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 455, in chimerax_intercept session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\gui.py", line 423, in thread_safe func(*args, **kw) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 446, in defer cxcmd(session, topic) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd run(session, cmd) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\commands\run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 131, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 213, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 514, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\open_command\cmd.py", line 484, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core_formats\\__init__.py", line 37, in open return cxs_open(session, data, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 1027, in open session.restore(stream, path=path, resize_window=resize_window, combine=combine) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 765, in restore self.reset() File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\session.py", line 552, in reset sm.reset_state(container, self) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seqalign\manager.py", line 273, in reset_state alignment._destroy() File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seqalign\alignment.py", line 724, in _destroy self._notify_observers(self.NOTE_DESTROYED, None) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seqalign\alignment.py", line 823, in _notify_observers recipient.alignment_notification(note_name, note_data) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\tool.py", line 471, in alignment_notification self.delete() File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\tool.py", line 509, in delete self.region_manager.destroy() ^^^^^^^^^^^^^^^^^^^ AttributeError: 'SequenceViewer' object has no attribute 'region_manager' AttributeError: 'SequenceViewer' object has no attribute 'region_manager' File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\tool.py", line 509, in delete self.region_manager.destroy() ^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. > open > D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise/tsa_taxol_ChainB.pdb > D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise/tsaGDP-ChainH.pdb Summary of feedback from opening D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise/tsa_taxol_ChainB.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 GLY D 10 HIS D 28 1 19 Start residue of secondary structure not found: HELIX 2 2 ASP D 41 ASP D 45 1 5 Start residue of secondary structure not found: HELIX 3 3 ILE D 47 VAL D 49 1 3 Start residue of secondary structure not found: HELIX 4 4 THR D 55 GLY D 57 1 3 Start residue of secondary structure not found: HELIX 5 5 GLY D 71 SER D 78 1 8 53 messages similar to the above omitted PDB SEQRES record for chain B is incomplete. Ignoring input sequence records as basis for sequence. Summary of feedback from opening D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise/tsaGDP-ChainH.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 GLY D 10 HIS D 28 1 19 Start residue of secondary structure not found: HELIX 2 2 ASP D 41 GLN D 43 1 3 Start residue of secondary structure not found: HELIX 3 3 ILE D 47 VAL D 49 1 3 Start residue of secondary structure not found: HELIX 4 4 THR D 55 GLY D 57 1 3 Start residue of secondary structure not found: HELIX 5 5 GLY D 71 SER D 78 1 8 245 messages similar to the above omitted PDB SEQRES record for chain H is incomplete. Ignoring input sequence records as basis for sequence. Chain information for tsa_taxol_ChainB.pdb #1 --- Chain | Description B | No description available J | No description available Chain information for tsaGDP-ChainH.pdb #2 --- Chain | Description H | No description available Associated tsa_taxol_ChainB.pdb chain J to tsa_taxol_ChainM-for_b3.pdb, chain M with 0 mismatches Traceback (most recent call last): File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\triggerset.py", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seqalign\alignment.py", line 427, in <lambda> self.associate([s for s in models if isinstance(s, AtomicStructure)], force=False)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seqalign\alignment.py", line 394, in associate self._notify_observers(note_name, note_data) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seqalign\alignment.py", line 823, in _notify_observers recipient.alignment_notification(note_name, note_data) File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\tool.py", line 482, in alignment_notification self.seq_canvas.alignment_notification(note_name, note_data) ^^^^^^^^^^^^^^^ AttributeError: 'SequenceViewer' object has no attribute 'seq_canvas' Error processing trigger "add models": AttributeError: 'SequenceViewer' object has no attribute 'seq_canvas' File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\tool.py", line 482, in alignment_notification self.seq_canvas.alignment_notification(note_name, note_data) ^^^^^^^^^^^^^^^ See log for complete Python traceback. > ui tool show "Color Actions" > set bgColor white > hide (protein|nucleic) target a > cartoon hide > show ((protein&@ca)|(nucleic&@p)) target ab > size pseudobondRadius 0.3 Changed 3861 pseudobond radii > ui tool show Matchmaker > select #1/B:1-500, select #2/H:1-500 6673 atoms, 6823 bonds, 856 pseudobonds, 858 residues, 4 models selected > ui tool show Matchmaker > matchmaker #!2 & sel to #1 & sel Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker tsa_taxol_ChainB.pdb, chain B (#1) with tsaGDP-ChainH.pdb, chain H (#2), sequence alignment score = 1860.7 RMSD between 428 pruned atom pairs is 0.554 angstroms; (across all 429 pairs: 0.574) > matchmaker #!2 & sel to #1 & sel showAlignment true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker tsa_taxol_ChainB.pdb, chain B (#1) with tsaGDP-ChainH.pdb, chain H (#2), sequence alignment score = 1860.7 Alignment identifier is 3 Showing conservation header ("seq_conservation" residue attribute) for alignment 3 Hiding conservation header for alignment 3 Chains used in RMSD evaluation for alignment 3: tsa_taxol_ChainB.pdb #1/B, tsaGDP-ChainH.pdb #2/H Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3 RMSD between 428 pruned atom pairs is 0.554 angstroms; (across all 429 pairs: 0.574) > sequence align 3 program muscle replace true Webservices job id: IQNVBUXS55PN73LQ > ui tool show "Render/Select by Attribute" > color byattribute r:seq_rmsd #!1 target sabc palette 0,blue:0,white:8,red 16808 atoms, 2151 residues, atom seq_rmsd range 0.0502 to 58 C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py:1944: RuntimeWarning: invalid value encountered in divide color = numpy.sum(colors, axis=0) / len(colors) C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py:1954: RuntimeWarning: invalid value encountered in cast brush = QBrush(QColor(*color.astype(int)), Qt.SolidPattern) Traceback (most recent call last): File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\triggerset.py", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 1895, in update_swatches block = block.next_block ^^^^^^^^^^^^^^^^ AttributeError: 'SeqBlock' object has no attribute 'next_block' Error processing trigger "changes done": AttributeError: 'SeqBlock' object has no attribute 'next_block' File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 1895, in update_swatches block = block.next_block ^^^^^^^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\triggerset.py", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 1895, in update_swatches block = block.next_block ^^^^^^^^^^^^^^^^ AttributeError: 'SeqBlock' object has no attribute 'next_block' Error processing trigger "changes done": AttributeError: 'SeqBlock' object has no attribute 'next_block' File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 1895, in update_swatches block = block.next_block ^^^^^^^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\triggerset.py", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 1895, in update_swatches block = block.next_block ^^^^^^^^^^^^^^^^ AttributeError: 'SeqBlock' object has no attribute 'next_block' Error processing trigger "changes done": AttributeError: 'SeqBlock' object has no attribute 'next_block' File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 1895, in update_swatches block = block.next_block ^^^^^^^^^^^^^^^^ See log for complete Python traceback. > color #2 #e5eaebff > select clear Traceback (most recent call last): File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\triggerset.py", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 1895, in update_swatches block = block.next_block ^^^^^^^^^^^^^^^^ AttributeError: 'SeqBlock' object has no attribute 'next_block' Error processing trigger "changes done": AttributeError: 'SeqBlock' object has no attribute 'next_block' File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 1895, in update_swatches block = block.next_block ^^^^^^^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\triggerset.py", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 1895, in update_swatches block = block.next_block ^^^^^^^^^^^^^^^^ AttributeError: 'SeqBlock' object has no attribute 'next_block' Error processing trigger "changes done": AttributeError: 'SeqBlock' object has no attribute 'next_block' File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site- packages\chimerax\seq_view\seq_canvas.py", line 1895, in update_swatches block = block.next_block ^^^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 3.3.0 - Build 27.20.100.9126 OpenGL renderer: Intel(R) UHD Graphics 620 OpenGL vendor: Intel Python: 3.11.4 Locale: en_US.cp1252 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: windows Manufacturer: Dell Inc. Model: Precision 3540 OS: Microsoft Windows 10 Enterprise (Build 19044) Memory: 16,985,317,376 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i5-8365U CPU @ 1.60GHz OSLanguage: en-US Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2024.6.2 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 comtypes: 1.4.1 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 24.1 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pywin32: 306 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 WMI: 1.5.1
Change History (2)
comment:1 by , 7 months ago
Component: | Unassigned → Sessions |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → RMSD header index error when restoring session |
comment:2 by , 7 months ago
Resolution: | → can't reproduce |
---|---|
Status: | accepted → closed |
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